User: ariel.balter

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ariel.balter10
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Posts by ariel.balter

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Benchmark - Comparison of Different NGS Mappers
... Good point @joe.cornish826. The OP used a data presentation style known to be a poor practice in order to show barely perceptible differences in data which is reported as a single number taken from a process that has a random component. They have no way of knowing if the differences are a complete f ...
written 5 weeks ago by ariel.balter10
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Answer: A: Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak callin
... In my case, I can ask the lab that did the sequencing, and they can tell me EXACTLY what the fragment size distribution is. I would try talking to them. The fragment size reported by the lab that did the PCR is undoubtedly going to be better than any software estimate. ...
written 6 weeks ago by ariel.balter10
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Answer: A: sicer chip seq analysis
... You might want to look into SICER's new incarnation in [EPIC](https://github.com/biocore-ntnu/epic). You will find it much more accessible. And the creator is very responsive to issues on GitHub and answering questions if they are posted here or on Stackoverflow. ...
written 6 weeks ago by ariel.balter10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... Looks like it is still trying: balter@server:~$ which python /home/.../Applications/miniconda3/bin/python balter@server:~$ python -V Python 3.5.2 balter@server:~$ conda install tophat Fetching package metadata ............. Solving package specifications: .......... ...
written 9 weeks ago by ariel.balter10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... Hi @Devon--that's great! Just to clarify: is this for the `tophat` code, the `bowtie2` code, or the conda recpie? ...
written 9 weeks ago by ariel.balter10
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MACS2 coverage calculations
... This relates to https://www.biostars.org/p/232347/ I'm trying to understand the output `macs2 callpeak` gives. As you can see, there are some identical coordinate ranges for which macs gives multiple, different fold changes, p-values, and q-values. However, when I calculate their coverage using `be ...
macs2 chip-seq written 9 weeks ago by ariel.balter10
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MACS2 Narrow peak (narrowPeak) output format
... According to the [macs2 documentation](https://github.com/taoliu/MACS#call-peaks), column 7 of the `*.narrowPeak` output bedfiles is supposed to be the fold change. However, using `bedtools multicov` I get a different result. $ bedtools multicov -bams ../bam/mock_lsd1_A.bam ../bam/mock_input_A. ...
macs2 chip-seq written 9 weeks ago by ariel.balter10 • updated 6 weeks ago by Biostar ♦♦ 10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... I get the usual I/O error with using python 3 balter@server:...users/balter/tophat/test_data$ conda create --name bowtietest bowtie2=2.2.5 tophat Fetching package metadata ............. Solving package specifications: .......... Package plan for installation in environment .../ ...
written 9 weeks ago by ariel.balter10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... Thanks. My group is discussing this right now. I'm actually not the fusion person, but I was trying to get a working `conda` recipe going for them. Turns out to be two things: 1) python 3 incompatibility in conda recipe and 2) bowtie2 + tophat version incompatibility. https://github.com/bioconda/bio ...
written 9 weeks ago by ariel.balter10
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Tophat and Bowtie installed with Conda not working on test data.
... I created a python 2.7 environment using conda, and installed tophat and bowtie. I'm trying the test data as specified here: https://ccb.jhu.edu/software/tophat/tutorial.shtml#inst However, I get the following error: balter@server3:/.../users/balter/tophat/test_data$ source activate p27 ( ...
tophat miniconda anaconda conda bowtie written 9 weeks ago by ariel.balter10

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